Last updated on 2025-03-22 17:51:30 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.99.0 | 1.73 | 25.70 | 27.43 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.99.0 | 1.57 | 20.40 | 21.97 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.99.0 | 46.33 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.99.0 | 57.26 | OK | |||
| r-devel-macos-arm64 | 0.99.0 | 26.00 | OK | |||
| r-devel-macos-x86_64 | 0.99.0 | 49.00 | OK | |||
| r-devel-windows-x86_64 | 0.99.0 | 4.00 | 46.00 | 50.00 | OK | |
| r-patched-linux-x86_64 | 0.99.0 | 1.81 | 24.92 | 26.73 | OK | |
| r-release-linux-x86_64 | 0.99.0 | 1.78 | 23.94 | 25.72 | ERROR | |
| r-release-macos-arm64 | 0.99.0 | 25.00 | OK | |||
| r-release-macos-x86_64 | 0.99.0 | 40.00 | OK | |||
| r-release-windows-x86_64 | 0.99.0 | 3.00 | 48.00 | 51.00 | OK | |
| r-oldrel-macos-arm64 | 0.99.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.99.0 | 44.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.99.0 | 4.00 | 46.00 | 50.00 | OK |
Version: 0.99.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘DEHOGT.Rmd’ using rmarkdown
Quitting from DEHOGT.Rmd:54-75 [exampleWorkflow]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `{
genewise_data <- data[i, ]
if (!is.null(covariates)) {
adjust <- covariates[i, ] %*% beta
} else {
adjust <- 0
}
genewise_dataframe <- data.frame(count = genewise_data, treatment = treatment,
size_factors = size_factors, adjust = rep(adjust, num_samples))
model_formula <- as.formula(
"count ~ treatment + offset(log(size_factors)) + offset(adjust)")
if (dist == "qpois") {
model <- glm(formula = model_formula, family = quasipoisson(), data = genewise_dataframe)
coefficients <- coef(summary(model))[2, "Estimate"]
p_values <- coef(summary(model))[2, "Pr(>|t|)"]
padj_values <- p.adjust(p_values, method = "BH")
log2fold <- log(exp(abs(coefficients)), base = 2)
} else if (dist == "negbin") {
model <- glm.nb(formula = model_formula, data = genewise_dataframe)
coefficients <- coef(summary(model))[2, "Estimate"]
p_values <- coef(summary(model))[2, "Pr(>|z|)"]
padj_values <- p.adjust(p_values, method = "BH")
log2fold <- log(exp(abs(coefficients)), base = 2)
}
c(coefficients, p_values, padj_values, log2fold)
}`:
! task 1 failed - "subscript out of bounds"
---
Backtrace:
▆
1. └─DEHOGT::dehogt_func(data, treatment, num_cores = 2)
2. └─... %dopar% ...
3. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'DEHOGT.Rmd' failed with diagnostics:
task 1 failed - "subscript out of bounds"
--- failed re-building ‘DEHOGT.Rmd’
SUMMARY: processing the following file failed:
‘DEHOGT.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64